Merge and resolve conflicts.

client/README.md

@@ -41,11 +41,8 @@ for inspection of live javascript to facilitate debugging, use:
 
     make client-production-maps
 
-Important Note: The development branch of Galaxy does not include client script
-artifacts, and these should not be committed.  When issuing a PR to a stable
-branch, please run "make client-production-maps", and include those artifacts.
-Or, if you'd rather, include only the /client source changes and build
-artifacts can be added by maintainers on merge.
+Important Note: The Galaxy repository does not include client script artifacts,
+and these should not be committed.
 
 
 Automatic Rebuilding (Watch Mode)

client/galaxy/scripts/components/DisplayStructured.vue

@@ -93,19 +93,16 @@ export default {
 .bold {
     font-weight: bold;
 }
-
 .light {
     font-weight: lighter;
     color: grey;
 }
 .right-aligned {
     text-align: right;
 }
-
 .clickable {
     cursor: pointer;
 }
-
 .workflow {
     border: solid gray 1px;
     margin-bottom: 1%;
@@ -120,64 +117,39 @@ export default {
 .workflow > .body {
     border-top: solid gray 1px;
 }
-.workflow > .body > .toolForm {
+.workflow > .body > .tool {
     border: 0px;
     margin: 0;
 }
-
-div.toolForm {
-    border-width: 1px;
-    border-radius: 0px;
-    margin-bottom: 1%;
+div.tool {
+    margin-bottom: 5px;
+    border: 1px solid gray;
 }
-.toolForm > .header {
-    background-color: #ebd9b2;
+.tool > .header {
     padding: 5px 10px;
 }
-.workflow div.toolForm:not(:first-child) .header {
-    border-top: 1px solid #d6b161;
-}
-div.toolFormTitle {
-    padding: 0px 0px 4px 0px;
-    margin: 0px 0px 4px 0px;
-    border: 0px;
-    background-color: transparent;
-    border-bottom: 1px solid #d6b161;
-}
-/* down from EBD9B2 --> 90743A */
-.toolFormTitle > .light {
-    color: #90743a;
-}
-.toolForm em {
-    color: #90743a;
-}
-
 .job-inputs {
     margin: 0px 6px 0px 6px;
     text-align: left;
 }
 .job-inputs td:nth-child(1) {
     text-align: right;
     font-weight: lighter;
-    color: #90743a;
+    color: gray;
 }
 .job-inputs td:nth-child(1):after {
     content: ":";
 }
 .job-inputs td:nth-child(2) {
     padding-left: 4px;
 }
-.job-inputs em {
-}
-
 .job-inputs-show {
     float: right;
 }
-
 .copied-from {
     border: 1px solid lightgrey;
     border-width: 1px 1px 0px 1px;
-    margin-bottom: 1%;
+    margin-bottom: 5px;
 }
 .copied-from .header {
     border-bottom: 1px solid lightgrey;
@@ -187,19 +159,4 @@ div.toolFormTitle {
 .copied-from .header a {
     color: #888;
 }
-
-.dataset.hda {
-    min-height: 37px;
-    border-width: 0px 0px 1px 0px;
-}
-.toolFormBody > .dataset.hda:last-child {
-    border-bottom-width: 0px;
-}
-.dataset.hda:first-child {
-    border-top: 1px solid #d6b161;
-}
-.dataset.hda .dataset-title-bar {
-    padding-top: 8px;
-    padding-left: 10px;
-}
 </style>

client/galaxy/scripts/components/Sharing.vue

@@ -1,7 +1,7 @@
 <template>
     <div v-if="ready">
         <h2>Share or Publish {{model_class}} `{{item.title}}`</h2>
-        <b-alert variant="danger" :show="err_msg">
+        <b-alert :show="show_danger" variant="danger" dismissible>
             {{ err_msg }}
         </b-alert>
         </br>
@@ -53,9 +53,17 @@
             <div v-else>
                 <p>This {{model_class_lc}} is currently restricted so that only you and the users listed below can access it. You can:</p>
                 <b-button @click="setSharing('make_accessible_via_link')">Make {{model_class}} Accessible via Link</b-button>
+                <span v-if="has_possible_members" class="chkk">
+                Also make all objects within the {{model_class}} accessible.
+                <input type="checkbox" v-model="make_members_public" id="chk_make_members_public">
+                </span>
                 <div class="toolParamHelp">Generates a web link that you can share with other people so that they can view and import the {{model_class_lc}}.</div>
                 <br/>
                 <b-button id="make_accessible_and_publish" @click="setSharing('make_accessible_and_publish')">Make {{model_class}} Accessible and Publish</b-button>
+                <span v-if="has_possible_members" class="chkk">
+                Also make all objects within the {{model_class}} accessible.
+                <input type="checkbox" v-model="make_members_public" id="chk_make_members_public">
+                </span>
                 <div class="toolParamHelp">Makes the {{model_class_lc}} accessible via link (see above) and publishes the {{model_class_lc}} to Galaxy's <a :href="published_url" target="_top">Published {{plural_name}}</a> section, where it is publicly listed and searchable.</div>
             </div>
             <br/><br/>
@@ -131,6 +139,12 @@ export default {
         },
         slug_url() {
             return `${Galaxy.root}${this.model_class_lc}/set_slug_async/?id=${this.id}`;
+        },
+        has_possible_members() {
+            return ["history"].indexOf(this.model_class_lc) > -1;
+        },
+        show_danger() {
+            return this.err_msg !== null;
         }
     },
     data() {
@@ -147,7 +161,8 @@ export default {
                 published: false,
                 users_shared_with: []
             },
-            share_fields: ["email", { key: "id", label: "" }]
+            share_fields: ["email", { key: "id", label: "" }],
+            make_members_public: false
         };
     },
     created: function() {
@@ -180,13 +195,20 @@ export default {
                 .catch(error => (this.err_msg = error.response.data.err_msg));
         },
         setSharing: function(action, user_id) {
+            let data = {
+                action: action,
+                user_id: user_id
+            };
+            if (this.has_possible_members) {
+                data.make_members_public = this.make_members_public;
+            }
             axios
-                .post(`${Galaxy.root}api/${this.plural_name_lc}/${this.id}/sharing`, {
-                    action: action,
-                    user_id: user_id
-                })
+                .post(`${Galaxy.root}api/${this.plural_name_lc}/${this.id}/sharing`, data)
                 .then(response => {
                     Object.assign(this.item, response.data);
+                    if (response.data.skipped) {
+                        this.err_msg = "Some of the items within this object were not published due to an error.";
+                    }
                 })
                 .catch(error => (this.err_msg = error.response.data.err_msg));
         },
@@ -233,3 +255,8 @@ export default {
     }
 };
 </script>
+<style>
+.chkk {
+    display: inline-block;
+}
+</style>

client/galaxy/scripts/components/admin/BaseGrid.vue

@@ -1,9 +1,9 @@
 <template>
-  <div class="toolForm">
-    <div class="toolFormTitle">
+  <div class="card">
+    <div class="card-header">
       <slot name="title">{{ title }}</slot>
     </div>
-    <div class="toolFormBody">
+    <div class="card-body">
       <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
         <slot name="columns">
           <th v-for="column in columns" bgcolor="#D8D8D8">{{ column.text }}</th>
@@ -41,3 +41,8 @@ export default {
     }
 };
 </script>
+<style>
+.card-body {
+    overflow: auto;
+}
+</style>

client/galaxy/scripts/layout/scratchbook.js

@@ -12,28 +12,28 @@ import _l from "utils/localization";
 
 export default Backbone.View.extend({
     initialize: function(options) {
-        var self = this;
         options = options || {};
         this.frames = new Frames.View({ visible: false });
         this.setElement(this.frames.$el);
+        this.active = false;
         this.buttonActive = options.collection.add({
             id: "enable-scratchbook",
             icon: "fa-th",
             tooltip: _l("Enable/Disable Scratchbook"),
-            onclick: function() {
-                self.active = !self.active;
-                self.buttonActive.set({
-                    toggle: self.active,
-                    show_note: self.active,
-                    note_cls: self.active && "fa fa-check"
+            onclick: () => {
+                this.active = !this.active;
+                this.buttonActive.set({
+                    toggle: this.active,
+                    show_note: this.active,
+                    note_cls: this.active && "fa fa-check"
                 });
-                if (!self.active) {
-                    self.frames.hide();
+                if (!this.active) {
+                    this.frames.hide();
                 }
             },
-            onbeforeunload: function() {
-                if (self.frames.length() > 0) {
-                    return `You opened ${self.frames.length()} frame(s) which will be lost.`;
+            onbeforeunload: () => {
+                if (this.frames.length() > 0) {
+                    return `You opened ${this.frames.length()} frame(s) which will be lost.`;
                 }
             }
         });
@@ -43,28 +43,28 @@ export default Backbone.View.extend({
             tooltip: _l("Show/Hide Scratchbook"),
             show_note: true,
             visible: false,
-            onclick: function(e) {
-                if (self.frames.visible) {
-                    self.frames.hide();
+            onclick: e => {
+                if (this.frames.visible) {
+                    this.frames.hide();
                 } else {
-                    self.frames.show();
+                    this.frames.show();
                 }
             }
         });
         this.frames
-            .on("add remove", function() {
-                if (this.visible && this.length() === 0) {
-                    this.hide();
+            .on("add remove", () => {
+                if (this.frames.visible && this.frames.length() === 0) {
+                    this.frames.hide();
                 }
-                self.buttonLoad.set({
-                    note: this.length(),
-                    visible: this.length() > 0
+                this.buttonLoad.set({
+                    note: this.frames.length(),
+                    visible: this.frames.length() > 0
                 });
             })
-            .on("show hide ", function() {
-                self.buttonLoad.set({
-                    toggle: this.visible,
-                    icon: (this.visible && "fa-eye") || "fa-eye-slash"
+            .on("show hide ", () => {
+                this.buttonLoad.set({
+                    toggle: this.frames.visible,
+                    icon: (this.frames.visible && "fa-eye") || "fa-eye-slash"
                 });
             });
         this.history_cache = {};

client/galaxy/scripts/mvc/dataset/dataset-li-edit.js

@@ -5,6 +5,10 @@ import ANNOTATIONS from "mvc/annotation";
 import faIconButton from "ui/fa-icon-button";
 import BASE_MVC from "mvc/base-mvc";
 import _l from "utils/localization";
+import * as _ from "underscore";
+
+/* global Galaxy */
+/* global $ */
 
 //==============================================================================
 var _super = DATASET_LI.DatasetListItemView;
@@ -100,7 +104,7 @@ var DatasetListItemEdit = _super.extend(
                 faIcon: "fa-times",
                 classes: "delete-btn",
                 onclick: function() {
-                    self.$el.find(".icon-btn.delete-btn").tooltip('dispose');
+                    self.$el.find(".icon-btn.delete-btn").tooltip("dispose");
                     self.model["delete"]();
                 }
             });
@@ -260,32 +264,29 @@ var DatasetListItemEdit = _super.extend(
             }
 
             if (visualizations.length >= 1) {
-                var url = Galaxy.root + "visualizations?dataset_id=" + this.model.get("id");
-                return $("<a/>")
-                    .addClass("visualization-link icon-btn")
-                    .attr("href", url)
-                    .append($("<span/>").addClass("fa fa-bar-chart-o"))
-                    .on("click", function(e) {
-                        Galaxy.frame.add({ url: url, title: "Visualization" });
-                        e.preventDefault();
-                    });
+                let dsid = this.model.get("id");
+                let url = Galaxy.root + "visualizations?dataset_id=" + dsid;
+                return faIconButton({
+                    title: _l("Visualize this data"),
+                    href: url,
+                    classes: "visualization-link",
+                    faIcon: "fa-bar-chart-o",
+                    onclick: ev => {
+                        if (Galaxy.frame && Galaxy.frame.active) {
+                            ev.preventDefault();
+                            Galaxy.frame.add({ url: url, title: "Visualization" });
+                        } else if (Galaxy.router) {
+                            ev.preventDefault();
+                            Galaxy.router.push("visualizations", {
+                                dataset_id: dsid
+                            });
+                            Galaxy.trigger("activate-hda", dsid);
+                        }
+                    }
+                });
             }
         },
 
-        /** add scratchbook functionality to visualization links */
-        _addScratchBookFn: function($links) {
-            $links.click(ev => {
-                if (Galaxy.frame && Galaxy.frame.active) {
-                    Galaxy.frame.add({
-                        title: _l("Visualization"),
-                        url: $(this).attr("href")
-                    });
-                    ev.preventDefault();
-                    ev.stopPropagation();
-                }
-            });
-        },
-
         //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)
         /** Render the tags list/control */
         _renderTags: function($where) {
@@ -392,7 +393,7 @@ var DatasetListItemEdit = _super.extend(
 
         /** listener for item purge (in the messages section) */
         _clickPurgeLink: function(ev) {
-            if (confirm(_l("This will permanently remove the data in your dataset. Are you sure?"))) {
+            if (window.confirm(_l("This will permanently remove the data in your dataset. Are you sure?"))) {
                 this.model.purge();
             }
             return false;